Research workbench
Dictyostelium myosin S1DC (motor domain fragment) complexed with N- methyl-O-nitrophenyl aminoethyldiphosphate beryllium trifluoride.
Analyse Dictyostelium myosin S1DC (motor domain fragment) complexed with N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D1C
- Type
- protein
- Length
- 744 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myosin
- UniProt
- P08799
- Ligands
- NMQ, MG
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myosin | protein | 744 | 46% helix, 15% strand | P08799 |
Ligands and binding sites
- NMQ · N-methyl O-nitrophenyl aminoethyldiphosphate beryllium trifluoride · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1022 | 0.85 | 0.86 | 108 | MG, NMQ |
| 2 | 935 | 0.73 | 0.77 | 78 | empty |
| 3 | 101 | 0.50 | 0.82 | 19 | empty |
| 4 | 151 | 0.44 | 0.75 | 27 | empty |
| 5 | 88 | 0.41 | 0.78 | 18 | empty |
Compared structures
- 1D1C · Dictyostelium myosin S1DC (motor domain fragment) complexed with N-methyl-O-nitrophenyl… · the same entry in another collection · chain A against A, TM-score 1.00
- P08799 · AlphaFold monomer V2.0 prediction for myosin-2 heavy chain (P08799) · a predicted model of the same protein · chain A against A, TM-score 0.89
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P08799
- Elsewhere: RCSB PDB 1D1C · PDBe 1D1C · UniProt P08799
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